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revision 1.1397 by jmc, Tue Mar 15 00:25:14 2011 UTC revision 1.1596 by gforget, Mon Feb 13 23:45:41 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice :
8      - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula.EQ.
9      1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
10      - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
11      - add permanent SItflux diag that corresponds to TFLUX but includes
12      ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
13      - allow activation/testing of a fix for suspected missing term in
14      ocn-ice heat budget (to be confirmed). To test this, you want to
15      undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
16      SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
17      - no change in results, fwd or ad.
18    o global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.
19      - switch to variable freezing point.
20           Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
21      - bug fix : the sublimation term that was missing is now activated.
22           Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
23      - bug fix : flooding sign term for SIsal0.NE.0.
24           Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
25    o pkg/seaice:
26      - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
27     is now the default, and the old default constant freezing point is recovered with
28     SEAICE_tempFrz0    = -1.96,
29     SEAICE_dTempFrz_dS = 0.,
30      - retire SEAICE_freeze that was the old way of specifycing the constant freezing point.
31      - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
32      - bug fix (thanks to M. Losch) : the sublimation term that was missing is now
33     activated. To reproduce old results that had this bug define SEAICE_DISABLE_SUBLIM.
34      - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211)
35     was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
36      - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in
37     seaice_growth r149 for legacy branch (no results change).
38      - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code from I. Fenty).
39      - results did not change except for global_ocean.cs32x15, mostly due to the switch
40      to variable freezing point (see above item for detail).
41    o pkg/thsice:
42      - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
43        seawater freezing in thsice_calc_thickn (not used).
44    o pkg/seaice: turbulent flux term specification via run time params.
45      - replace CPP switches with run time switches to facilitate testing
46      - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
47      - added runtime parameter : SEAICEturbFluxFormula
48      - move Mcphee constants to SEAICE_PARAMS.h
49      - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
50        SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove
51        seaice_summary call (moved to seaice_init_fixed)
52      - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
53        SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
54      - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).
55      - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).
56      - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
57            CPP switch, same computation as before for the different options.
58      - change results at the truncation level.
59    o pkg/seaice:
60      - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
61        useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
62        SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
63      - update verification/*/input*/data.seaice:
64        to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
65        code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
66        and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
67        set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
68    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
69      - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
70        algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
71        difference in results only due to machine truncation.
72      - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
73        MaykutPolySatVap; keep MIN_LWDOWN.
74      - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
75      - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
76        + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
77    o pkg/salt_plume:
78      - isolate saltPlumeFlux array exch into a specific S/R called from
79        do_oceanic_phys.F
80      - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
81    o verification:
82      - move untested set-up to MITgcm_contrib/verification_other.
83    o pkg/seaice:
84      - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
85    o pkg/seaice:
86      - seaice_solve4temp.F (keeping results unchanged):
87        * add 2 future run-time params to select which saturation vapor pressure
88          formula is used and how post-iteration fluxes are set.
89          Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
90        * New piece of code (not used) to update surf. atmos. heat flux F_ia using
91          the linearized expression to stay consistent with tsurf finding.
92      - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
93        can be < 0.
94    o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
95      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
96        conductive heat flux F_c , and add it explicitly when updating tsurf as
97        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
98        so that now F_ia has a consistent meaning through the entire routine.
99        This causes differences at truncation level: update output of fwd exp.
100        global_ocean.cs32x15.seaice.
101    o pkg/seaice:
102      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
103        of arrays, sign/direction of fluxes; no effect on results.
104      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
105        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
106        note: this should have been done before changing celsius2K default.
107      - to keep results unchanged, add back old value of celsius2K in verification
108        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
109      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
110        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
111        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
112        freezing temp is consistent with value in seaice_growth.F ; this causes
113        differences at machine truncation level: update lab_sea AD output (3/4).
114    o pkg/seaice:
115      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
116        and climsst/sss even when using seaice (to prevent calculation that might
117        use SST on land); does not affect any verification exp.
118      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
119        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
120    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
121      over land (non-legacy code)
122    o vectorize salt_plume package:
123      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
124      - this code computes plumebk everywhere (also over land), thus requires
125        code to avoid divisions by zero and catch the case of kLev=Nr.
126      - efficiency of salt_plume_frac is still sub-optimal
127    o tools (genmake2):
128      - fix makefile NAME specification (option: -makefile NAME) by adding
129        "-f $MAKEFILE" in few places where it was missing including makedepend
130        command (contribution from Paul).
131    
132    checkpoint63i (2012/01/24)
133    o model/src:
134      - add factorized versions of some EOS code to find_rho.F,
135        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
136    o model/src:
137      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
138      - change default celsius2K from 273.16 to 273.15
139      - to keep results unchanged, add back old value of celsius2K in verification
140        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
141         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
142    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
143      to make TAF generate vectorizable code
144    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
145       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
146       have flags that do this more efficiently.
147    o pkg/diagnostics/diagstats_calc.F
148      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
149    o pkg/obcs (with exch2):
150      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
151        and remove code (in obcs_readparms.F) which was based on EXCH of indices
152        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
153    o pkg/exf and seaice exp:
154      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
155        so that switching off area & heff advection flags does not affect results.
156      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
157      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
158        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
159        results of verification experiments: 1D_ocean_ice_column(fwd),
160        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
161        and offline_exf_seaice (all 4).
162    o pkg/seaice:
163      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
164        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
165      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
166        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
167        not multi-dim advection;
168      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
169        SHORTWAVE_HEATING #undef.
170    o optim: make Makefile more robust (?)
171    o pkg/obcs:
172      * fix treatment of obcs_read_pickup for TAF
173    o pkg/shelfice:
174      * add missing initialisation of num_shifwflx
175      * new adjoint verification exp. for isomip
176      * change Prandtl and Schmidt numbers from generic formulations
177        (in terms of model diffus. and visc.) to separate runtime
178        parameters, with Holland and Jenkins (1999) default values.
179    o pkg/exf (interpolation):
180      - extended input field (2 rows) near the N & S poles:
181        * fill in with the symetric value (when even Nb of data in longitude)
182        * add average value at the poles only for scalar quantities ; for vector
183          component interpolation, skip the averaging and keep duplicated values,
184          unless the 2 components have same location (uvInterp=T) in which case
185          interpolate the 2 components together using S/R EXF_INTERP_UV.
186      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
187        together: this allows to account properly for local orientation when
188        averaging at N & S pole.
189      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
190        exf-interpolation near N & S poles. Undef by default.
191      - add debug check/print on 1rst iter if debugLevel >=2.
192    o pkg/exf:
193      - change masking flags definition (no longer "parameter"), put them in
194        common block and set them in S/R EXF_INIT_FIXED.
195      - change recognized masking flag from s,u,v to c,w,s since the mask
196        to use (maskC,W,S) depends on position on model grid and has little to
197        do with scalar/vector difference; fix masking if using P-coordinates.
198      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
199        and update results of exp. global_with_exf (x2).
200      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
201    o pkg/obcs
202      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
203    o pkg/exf (interpolation):
204      - assume periodicity in X only if input field cover full longitude range.
205      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
206        and should vectorise).
207      - fix input lat of the 2 added row (in case we provide N.pole data).
208    
209    checkpoint63h (2011/12/30)
210    o pkg/seaice:
211      - change declaration of UVM from _RL to _RS in order to get B-grid
212        uIce,vIce monitor when _RS = real*4
213    o pkg/offline:
214      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
215      - compute vertical velocity if not read from file (switch on exactConserv
216        & staggerTimeStep);
217      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
218    o verification:
219      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
220        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
221        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
222      - update output of exp. global_ocean.cs32x15.viscA4 after changing
223        grid-file angles (used here for coriolis-3d);
224      - remove (or gzip) few files not needed to run fizhi-cs experiments.
225    o pkg/exf (vector interpolation):
226      - rotate vector component toward local grid-axis orientation using grid-angles
227        (stored in GRID.h) instead of locally computed rotation angle; keep old code
228        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
229    o pkg/seaice:
230      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
231        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
232    o pkg/PKG_OPTIONS.h files:
233      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
234        outside of the #ifdef ALLOW_THISPKG / #endif block.
235      - update verification/*/code/PKG_OPTIONS.h files.
236    o add a verification experiment (offline_exf_seaice/input.seaice) that test
237      the B-grid LSOR solver
238    o pkg/seaice: sort out emissivity and long wave radiation step 2:
239      - add emissivity for snow and ice as new run-time parameters
240        (unfortunately) that default to the corresponding exf values; this
241        changes results in most verification experiments so that for backward
242        compatibility these parameter have to be set explicitly to inconsistent
243        values (ugly);
244      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
245        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
246        until we agree how to handle this bug properly
247    o pkg/exf (interpolation):
248      - add a set of run-time param ({inputfield}_interpMethod), one for
249        each interpolated input field, to select the interpolation method
250        with a value of zero switching off the interpolation;
251      - print interpolation parameters to standard output;
252      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
253        (to use instead runoff_interpMethod=0 in data.exf).
254      - simplify default setting of interpolation parameters (for all fields,
255        set position to match model grid cell-center position, leading to trivial
256        interpolation in case of regular Lat-Lon grid) and fix for the case of
257        non-uniform delY.
258    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
259       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
260       this factor is absolutely required, because the lw exitance (= out-going
261       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
262       where the reflectivity rho = 1-emissivity for conservation reasons. Once
263       this is established, we can remove the CPP-Flag (if we want to).
264    o pkg/seaice:
265      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
266        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
267      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
268        what the name implies (and not emissivity*BoltzmannConstant), this means
269        the old default value of 5.5e-8 now means
270        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
271        S/R exf_readparms
272      - FV-discretization of the B-grid LSOR solver, turn on with
273        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
274        of the calling routine dynsolver, so that B and C-grid code look a
275        little more alike.
276      - fix index bugs in ostres.F (B-grid code)
277    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
278    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
279      default for SEAICE_emissivity, if useEXF; requires setting a wrong
280      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
281      backward compatiblity
282    o model/src: use sigmaR in calc_ivdc
283    
284    checkpoint63g (2011/12/16)
285    o pkg/seaice/seaice_growth.F:
286      fix heat conservation of the coupled ocean-seaice system.
287      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
288      solid vs liquid water treatment is resolved via QNET.
289    o pkg/seaice/seaice_growth.F:
290      add missing term for sublimation in saltFlux, which was breaking conservation.
291    o pkg/seaice/seaice_model.F:
292      Remove this patholigical case treatment in evolution branch,
293      where it is un-necessary and breaks conservation.
294      Update global_ocean.cs32x15/results accordingly for
295      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
296    o model/src:
297      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
298      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
299    o pkg/obcs:
300      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
301      tendency for temperature and salinity that is then applied to update
302      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
303      horizontal advection and diffusion contributions on the boundary (in
304      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
305      removing the mask in S/R timestep_tracer. The advantage of this approach is
306      that the updated tracer values include contributions from the surface
307      forcing and vertical diffusion.
308      This modification changes exp4.stevens because of vertical diffusion.
309    o model/src:
310      change non-curvilinear grid setting to also work with exch2 + blank tiles:
311      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
312        face dimensions.
313      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
314        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
315        and INI_SPHERICAL_POLAR_GRID.
316      change test-experiment global_ocean.90x40x15:
317      - split the domain in many more tiles (9x4 tiles of 10x10 each);
318      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
319      - update results of both test (std & dwnslp).
320    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
321       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
322    o model/src:
323      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
324        and fix initialisation when using sigma-coords.
325    o model/src:
326     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
327       to their current value at the beginning of forward_step.F": add a new run-time
328       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
329     - set doResetHFactors=T in the following test exp:
330        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
331        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
332        and tutorial_global_oce_in_p (nonLinFS in p)
333    o pkg/ecco
334      - added IES cost term
335    o verification/advect_xz
336      - scale down the depth by 1/100 (from 200 km to just 2.km)
337      - add secondary test using divergent flow, r-star and implicit vertical advection.
338      - add note (check_conserve_TS.txt) and matlab script to check global
339        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
340    o pkg/rbcs:
341      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
342    o pkg/obcs (Stevens BCs):
343      - fix various problems in the phase speed computations of the Stevens
344        boundary conditions:
345        - sign error for western and southern boundaries,
346        - time tendencies were underestimated by factor of dTracerLev and some just
347          zero (for multidim advection schemes) -> now estimate time tendencies
348          from difference between previous (n) time level and the one before (n-1);
349          this requires storing a field per tracer per boundary, also in the pickup
350          files.
351        - replace deltaTmom in cflMer/Zon computation with dTracerLev
352        - set default phase velocity to cflMer/Zon
353      - update verification experiment exp4.stevens
354    o pkg/generic_advdiff (implicit_r):
355      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
356        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
357      - fix implicit vertical diffusion or advection with NonLin FreeSurf
358        (was using current recip_hFacC instead of future recip_hFacC): set future
359        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
360        solver S/R ;
361      - fill diagnostics of vertical advective fluxes (computed from tendency)
362        when using implicit vert. advection;
363      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
364         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
365         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
366         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
367    o pkg/diagnostics:
368      - add diags for T & S tendency which goes through Adams-Bashforth.
369    
370    checkpoint63f (2011/11/30)
371    o pkg/obcs/obcs_calc_stevens.F:
372      - join some loops to reduce number of if-statements
373      - fix a bug in code for northern and southern boundaries.
374    o pkg/seaice/seaice_init_varia.F
375      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
376        caused zero ice-velocities for the B-grid code
377    o pkg/seaice/seaice_init_fixed.F
378      - fix a bug in the initialisation of the second metric terms
379        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
380      - this affects all seaice configurations with useCurviLinearGrid = .true.
381        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
382        = .true. (default)
383      - the only verification experiment affected is global_ocean.cs32x15:
384        icedyn, seaice, and seaice_dynmix (AD)
385    o pkg/thsice/thsice_diagnostics_state.F
386      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
387        not contain garbage that can lead to surprises in diagstats_calc.F
388    o model/src:
389      - move bi,bj loops inside INTEGR_CONTINUITY ;
390      - call INTEGR_CONTINUITY directly from forward_step.F
391        (previously called from momentum_correction_step.F)
392      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
393        forward_step.F and pkg/ecco/the_main_loop.F
394    o model/src/do_oceanic_phys.F:
395      - reset addMass to zero only if useICEFRONT ;
396      - separated k-loop for rhoInSitu calculation ;
397      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
398        and at constant T,S (= WdRHOdP);
399      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
400        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
401        transport of locally-referenced potential density);
402        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
403    o gluemnc:
404      - replace ncrcat with ncks when adding variables to *.glob.nc
405      - change the way variables without record dimensions are handled so that
406        files that have variables with and without record variables can be glued:
407        add a record dimension with a new unique name to be able to differentiate
408        between variable with and without a-prior record dimensions. Remove
409        this record dimension before adding the variable to the *.glob.nc file.
410        This procedure automatically works also for grid.*.nc files that do not
411        have any record dimension.
412    o verification/cpl_aim+ocn:
413      - generate new reference output on baudelaire (gfortran, mpich2) (previously
414        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
415    o pkg/obcs/obcs_calc_stevens.F:
416      - add code for northern and southern boundaries.
417      - reorder some loops to save some operations and so that drFBar can be scalar
418    o model/src:
419      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
420        truncation) and add diagnostics for Adams-Bashforth tendency increment.
421      - update test-exp. AD output:
422        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
423      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
424        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
425        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
426        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
427        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
428        tutorial_plume_on_slope.
429    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
430      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
431      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
432      does not even come with an F77 compiler anymore, this should not be
433      a limitation
434    
435    checkpoint63e (2011/11/06)
436    o pkg/seaice adjoint of LSR:
437      - substantially rework STORE dirs.
438      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
439        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
440        and only perform SOLV_MAX_FIXED adjoint iters.
441        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
442        always goes to same record, meaning that the last forward field will be
443        the one used in the adjoint - an approximation.
444      - now produces non-zero LSR-related gradients, and acceptable gradients for
445        An's zonal (x-z) test case (to be checked in)
446      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
447        (but these are screwed up by the thermodynamics in the first place);
448        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
449        output_adm.txt also reflects changes to seaice_lsr
450      - global_ocean.cs32x15:
451        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
452          (output_adm.seaice.txt was updated)
453        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
454          (output_adm.seaice_dynmix.txt)
455    o test-exp. exp4+stevens:
456      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
457    o pkg/seaice (lsr solver):
458      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
459        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
460      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
461      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
462        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
463      - compute (with new S/R) and print initial (+ free-driff sol. if available)
464        and final residual of linearised system.
465    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
466      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
467    o pkg/obcs: Stevens BCs (still only for east and west)
468      - fix Stevens BCs by using intermediate velocities of previous
469        time step as "baroclinic" contribution rather velocity of one grid cell
470        inside the boundaries; more consistent but makes the entire treatment
471        more complicated, requires new pickup files and two new S/Rs:
472        obcs_copy_uv_n and obcs_save_uv_n
473        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
474        (undefined by default)
475      - silently move computation of some grid factors into separate loops to
476        save some recomputations
477      - add a hack for non-linear free surface
478      - add a verification experiment to exp4 that tests this code
479    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
480    
481    checkpoint63d (2011/10/25)
482    o pkg/obcs + seaice-dynamics:
483      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
484        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
485        values (consistent with an implicit method).
486      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
487        return to older implementation (same results as before); note that none of
488        the "experimental" OBCS_SEAICE options are implemented in the new version.
489      - switch test exp. seaice_obcs to use new version (update output).
490    o pkg/seaice:
491      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
492      - add parenthesis in Water-Ice drag calculations (evp & lsr);
493      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
494        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
495      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
496        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
497    o pkg/layers:
498      - Include potential density as new coordinate (Thanks to David Munday)
499    o pkg/dic:
500      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
501        carbonate computation/output to CALC_PCO2_APPROX
502    o pkg/generic_advdiff
503      - make TAF generate code that vectorizes:
504        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
505    o model/src:
506      - improve vectorization also for adjoint code of
507        solve_tridiagonal and solve_pentadiagonal. As this requires up to
508        5 new 3D-fields, this code is only turned on for the combination of
509        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
510        for singular matrix check (only for TARGET_NEC_SX).
511      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
512        ALLOW_AUTODIFF. This flag now needs to be set outside of
513        solve_tri/pentadiagonal.F
514    o pkg/exf:
515      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
516        optional namelist EXF_NML_OBCS).
517      - add many debug-print (to trace down where pkg/cal error msg comes from)
518    o pkg/mom_vecinv/mom_vi_hdissip.F
519      - rearrange loops so that vectorization is improved and in particular
520        the adjoint routine vectorizes. The code is a little longer now, but I
521        think easier to read.
522        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
523    o pkg/seaice:
524      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
525    o pkg/exch2:
526      - alternative code (without tile x tile matrix) for cumulated (global) sum;
527        used as default; keep using matrix version in adjustment.cs-32x32x1.
528    o tools/build_options:
529      - after merging some MPI and/or multi-threads specific optfiles so that
530        the modified default optfile support both built (using genmake2 -mpi
531        for the MPI built, using genmake2 -omp for OpenMP built),
532        move now obsolete optfiles to tools/build_options/unsupported/
533       (add copy of email sent to support list in doc/optfiles_changes.txt)
534    
535    checkpoint63c (2011/09/28)
536    o pkg/ebm:
537      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
538        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
539    o pkg/seaice (SItracer pickup)
540    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
541      To be done:
542      - thorough testing of missing fields in S/R seaice_read_pickup
543      - thorough matching between generic tracers and specific fields used
544        (e.g. volume-weighted age, area-weighted age, salinity, ...)
545    o pkg/grdchk:
546      - all procs calculate and print finite-difference gradient (for testreport)
547      - change description output used by testreport;
548      - AD testing: also compare and report Finite-difference gradient;
549        => update all output_adm*.txt
550    o test exp. global_ocean_ebm:
551      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
552        and turn on exactConserve; update (fwd) output.
553    o pkg/seaice (LSR):
554      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
555      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
556        * identical results with non-CS topology (but save up to half of EXCH calls)
557        * no much changes in cs-32 verification tests since no ice at face edges
558         (differences due to convergence criteria, since nb of iterations changed)
559        * expect some differences on lat-lon-cap grid.
560        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
561    o pkg/exch2:
562      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
563        many tiles); until alternative coding is added, just add a stop.
564    o pkg/kpp:
565      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
566        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
567    o optfiles:
568      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
569        into corresponding standard one, which now support different build:
570        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
571      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
572    o pkg/obcs (seaice):
573      - add missing EXCH for uIce,vIce after applying OBCS;
574      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
575        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
576        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
577      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
578      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
579        and eedata.mth for MPI and mutlti-threaded testing.
580    o pkg/flt:
581      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
582      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
583      - fix pickup and trajectories + profiles output with multi-threads;
584      - add parameter to select group of fields to write along trajectory and
585        profile (default unchanged);
586      - only call PORT_RAND* function when flt_noise <> 0;
587      - add multi-threaded test for verification exp. flt_example.
588    o eesupp/src:
589      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
590      - USE_OMP_THREADING: check that number of threads (from eedata) matches
591        actual number (from env.var. setting).
592    o pkg/ebm:
593      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
594      - add multi-threaded test for verification exp. global_ocean_ebm
595    
596    checkpoint63b (2011/08/29)
597    o pkg/ebm:
598      - fix sign of runoff;
599      - update directly forcing fields (Qnet,EmPmR) to use standard
600        external_forcing_surf.F (remove ebm_forcing_surf.F);
601      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
602      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
603        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
604      - update global_ocean_ebm parameters file data and update output (fwd+ad).
605    o verification/matrix_example:
606      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
607        MPI and mutlti-threaded testing.
608    o pkg/matrix:
609      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
610      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
611      - fix for multi-threaded (remove DATA statement);
612      - use standard DIFFERENT_MULTIPLE function;
613      - add MATRIX_OPTIONS.h
614    o verification/matrix_example:
615       To allow to split the domain in several tiles, change the domain size
616        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
617        Western side) of land points.
618    o (*_)write_pickup:
619      - fix few bugs in mypackage_read/write_pickup.F
620      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
621        array of length 1 (was caught by compiler syntax-check).
622    o pkg/diagnostics (velocity potential solver):
623      - fix initialisation of main diagonal matrix (for overlap values)
624    o tools/build_options:
625      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
626        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
627      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
628        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
629        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
630        and use "-devel" testreport option for standard testing on baudelaire.
631    o pkg/grdchk:
632      - Assume that all gradient-check position are within the same tile
633        corresponding to global indices (iGloTile,jGloTile) and that
634        positions (i,j indices or nbeg) are local to this tile;
635      - set tile local-indices and proc. number according to tile global-indices;
636      - remove grdchkwhichproc from namelist (retired param);
637      - send adjoint gradient to all procs so that all procs print it to STDOUT;
638      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
639    o adding package bbl (Bottom Boundary Layer)
640      description in MITgcm/pkg/bbl/bbl_description.tex
641      example/test experiment in MITgcm_contrib/bbl
642    o adjoint verifications
643      - changed 5 experiments to multi-tiles
644        * global_ocean.90x40x15
645        * obcs_ctrl
646        * offline_exf_seaice
647        * tutorial_dic_adjoffline
648        * tutorial_tracer_adjsens
649        changed reference output for those that crossed tile boundaries
650        (changed choices of gradient check positions)
651      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
652      - temporary bug fix in grdchk_loc.F for obcs
653    o genmake2 & testreport
654      - add target "obj" (just for OBJFILES files) to Makefile;
655      - add option to specify FEXTRAFLAGS on command line.
656    o pkg/mypackage:
657      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
658    
659    checkpoint63a (2011/08/02)
660    o pkg/diagnostics (velocity potential):
661      - fix velocity-potential calculation when using OBCS: balance net inflow
662        at each level (new S/R OBCS_DIAG_BALANCE).
663      - fix some of the problems with OBCS in stream-function calculation.
664    o pkg/exf/exf_readparms.F
665      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
666        EXF_NML_OBCS) more consistent, so that you need not have these lists
667        in data.exf when they are not used.
668    o optim/optim_readdata.F:
669      - add some output about obcs variables that might help debugging
670      - add a check about nvarlength
671    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
672    o pkg/diagnostics (velocity potential):
673      - fix mask for OBCS (still problems in stream-function with OBCS);
674      - add specific parameter (default = main code CG2D params) for solver;
675      - in case of poor convergence, use solution corresponding to lowest residual.
676    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
677      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
678      and should be avoided where possible.
679    o model/src (rStar):
680      - include r* effect on reference-state (PhiRef) in totPhiHyd
681        (so that it's really the potential anomaly at the cell center);
682        affect solution only if z* with full pressure in EOS.
683      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
684        update output (because of z* in totPhiHyd and viscA4 changes);
685      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
686        @ constant r) until interpolation at constant r is implemented.
687    o pkg/diagnostics
688      - fix RCENTER diagnostics in case cell center is not at interface middle
689    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
690      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
691      that THETA and SALT are "conservative temperature" and "absolute
692      salinity"
693    o pkg/ctrl
694      - fix computation of endrec in s/r ctrl_init_rec
695      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
696    o pkg/seaice/seaice_growth.F
697      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
698        remove then obsolete STORE directives
699      - fix STORE directives for tice and tices, so that only the
700        appropriate part of the fields are stored (and not the entire
701        field); update global_ocean.cs32x15.seaice AD output.
702      - cosmetic changes: adjust CPP flags and indentation for better
703        legibilty
704    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
705      Chris Wilson)
706    o pkg/gmredi:
707       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
708       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
709    
710    checkpoint63  (2011/07/11)
711    o pkg/exch2:
712     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
713     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
714       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
715       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
716    o pkg/diagnostics:
717     - deal with pairs of post-processed diags which are computed together; in
718       particular, re-order list of diags within 1 file to save 2nd computation.
719     - add S/R to compute velocity stream-function (called after velocity-potential
720       calculation) from divergence free transport -> new diagnostics "PsiVEL".
721     - add parameter to select grid-point location where PsiVEL == 0.
722    o eesupp/src:
723       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
724       (specific S/R needed with exch2 topology - for now, just print an error msg)
725    o pkg/shelfice
726     - Implement friction velocity-dependent transfer coefficients following
727       Holland and Jenkins, JPO, 1999
728       Original code by M. Losch with small modifs.
729       Enable with CPP option SHI_ALLOW_GAMMAFRICT
730       and runtime flag SHELFICEuseGammaFrict
731    o verification lab_sea & global_ocean.cs32x15:
732     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
733       does not miss some dependencies (but is slower) and also works with many files
734       (default makedepend limitation for AD built).
735     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
736    o pkg/diagnostics:
737     - add run-time parameter "useMissingValue" (def=False) to fill land-point
738        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
739       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
740     - Extend the use of "missing_value" setting from data.diagnostics for the case
741       of counter-diagnostics (where fraction-weight is zero). This applies both to
742       MNC and MDS output files.
743    o pkg/seaice/seaice_growth.F:
744      - add 'a priori' cap of latent heat flux based on actual mass considerations
745        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
746        non-legacy seaice_solve4temp.
747      - add diagnostic of the residual sublimation freshwater flux (the freshwater
748        flux taken from the ocean if the total actual latent heat fluxes exceed
749        the maximum)
750      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
751       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
752      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
753       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
754      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
755      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
756    o verification 1D_ocean_ice_column:
757       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
758       update results
759    o pkg/diagnostics:
760     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
761       which are not filled-up but computed from other diags ; In this case, the mate
762       diag points to the primary (filled-up) diag to used for post processing.
763     - Update Velocity-potential computation using post-processed diag framework.
764     ==> Change the ordering of fields and time-periods in MDS output file
765       when using periodic averaging: now writes one time record with the full set
766       of fields for this time period, then the next time reccord (it used to be
767       one field with the full set of time records then the next field).
768         Note: this is now similar to NetCDF (MNC) output file. <==
769    
770    checkpoint62z (2011/06/21)
771    o adjoint monitor:
772     - Add adjoint monitor output for packages exf, seaice
773       and update relevant testreport output
774    o pkg/seaice:
775     - re-order diags inits so that they appear in order in available_diagnostics.log
776     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
777       area/heff/hsnow preceeding thermodynamic growth/melt.
778     - modified diag: SIdA; output actual effect, as the description states.
779     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
780     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
781       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
782        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
783     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
784     - added diagnostics for seaice generic tracers (SItr*).
785     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
786     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
787     I. Fenty: 18-Jun-2011:
788     Minor changes to seaice package:
789     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
790        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
791       - Differentiated "regularization variables" from "floor variables"
792        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
793        * hiceMin became SEAICE_hice_reg (old hiceMin)
794          (with _reg meaning regularization variable)
795       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
796        so as to ensure energy conservation when going between phases
797      - A22 was not used anywhere
798     2) Changed regularization procedure for heffActual and hsnowActual to ensure
799        well-boundedness and smooth adjoint in seaice_growth.F
800     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
801        because the old regularization always set heffActual >= 0.05 cm
802     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
803        on AREA when HEFF > 0.
804      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
805        requiring that DISABLE_AREA_FLOOR *not* be defined
806     Affected verifications:
807      - 1D_ocean_ice_column (output.txt output_adm.txt)
808      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
809    o pkg/diagnostics:
810      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
811      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
812        (was _RL, now integer) with option = 0 to retrieve all levels.
813      - add pieces of code to compute velocity potential at each level (new diagnostics
814        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
815        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
816      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
817        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
818        and in diagnostics_fract_fill.F (do not need a valid pointer for the
819        diagnostics counter-mate); check that definition of counter-diagnostic
820        includes a valid counter-mate (in diagnostics_set_levels.F).
821    o model/src (rStar):
822      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
823        affect solution only if z* with full pressure in EOS;
824        update output of test-exp global_ocean.90x40x15.
825    o pkg/seaice:
826      - introduce siEps=1e-5 parameter
827      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
828      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
829      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
830        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
831        as well as ice cover age and ridging index (attached to AREA).
832        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
833        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
834        Up to SItrMaxNum=3 tracers can be used simultaneously.
835    o pkg/salt_plume:
836      -introduce SPsalFRAC run time parameter that sets the fraction of the
837       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
838       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
839    o model debug options:
840      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
841        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
842      - Refine debug-msg printing selection (3 new levels):
843        debugMode  : controls printing of debug messages (sequence of S/R calls).
844        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
845         debLevZero =  0 ; /* level of disabled aux. msg printing */
846         debLevA =  1 ; /* level of minimum  aux. msg printing */
847         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
848         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
849         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
850         debLevE =  5 ; /* level of extensive debug printing */
851        New debugLevel default: with default debugMode value (=F),
852          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
853          and if debugMode=T, default debugLevel = 4 (debLevD).
854        Relation with previous settings:
855         debLevB (=2) corresponds to former debLevA (=1)
856         debLevD (=4) corresponds to former debLevB (=2)
857        Note:
858         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
859         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
860            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
861      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
862        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
863    o pkg/obcs:
864      - change OBCSfixTopo default from True to False (should not change the results);
865        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
866    o pkg/thsice:
867      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
868        2nd layer seaice sublimation (unlikely to happen)
869      - use Interior mask for OBCS in thsice_advection.F (similar to what is
870        done in gad_advection & seaice_advection).
871    o adjoint:
872      bug fix spotted by Gael Forget:
873      seaice_advection and thsice_advection still had
874      legacy CPP options to avoid CS corner updates for adjoint
875    o pkg/seaice:
876      => Change some of the defaults (2011/05/29):
877         - change SEAICEuseFluxForm default (from False to True)
878         - change DIFF1 default (from 0.004 m/s to 0. m/s)
879         And print warnings if DIFF1 is not set in data.seaice and centered
880          avection scheme is used without any diffusion.
881      also:
882      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
883      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
884      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
885        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
886        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
887      update results of test exp.:
888         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
889             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
890             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
891         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
892         seaice_obcs: output (SEAICEuseFluxForm=T)
893      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
894          for standard fwd & AD lab_sea tests (to keep the same output).
895    o pkg/seaice/seaice_growth.F:
896      - use Ian Fenty's capping formulas for actual ice
897      thickness thoughout EVOLUTION branch.
898      - put treatment pathological case #2) in CPP brackets
899      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
900      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
901    o pkg/seaice:
902      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
903      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
904      also pass fac as a param, which can be 1. (to update the tendency
905      field) or the time step (to update the field itself).
906      - seaice_advdiff.F: for multidim, call seaice_diffusion with
907      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
908      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
909      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
910      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
911    o pkg/seaice:
912      diffusion with centered advection scheme (diffus.F & advect.F):
913      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
914        to just compute the laplacian of input-field.
915      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
916      - fix flux-form version in diffus.F to conserve tracer.
917      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
918       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
919    
920    checkpoint62y (2011/05/26)
921    o pkg/seaice:
922     - seaice_growth.F : in EVOLUTION branch, always include
923       a_QSWbyATM_cover in qnet (as it should be).
924     - verification/global_ocean.cs32x15 : update results accordingly
925       (output.seaice.txt output_adm.seaice.txt).
926    o pkg/seaice + obcs:
927     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
928       equivalent of assuming no tracer gradient outside the OB region.
929       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
930     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
931       after changes above);
932     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
933       only at OB location (instead of over a band of OLx width).
934    o pkg/seaice:
935     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
936       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
937    o pkg/obcs:
938      - split header file "OBCS.h" into 4 separated files:
939        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
940       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
941         (contain no conditional statement which depends on OBCS options).
942      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
943        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
944    o ctrl, cost, grdchk & autodiff pkgs:
945      - make options file more standard (like other {PKG}_OPTIONS.h file but
946        with AD_CONFIG.h); clean-up some of the included header files.
947    o pkg/obcs:
948      - do not mask tracer when applying OB (tracer == 0 could generate problems)
949      - apply tracer OB values to tracer field only at OB location (instead of
950        over a band of OLx width)
951      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
952      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
953        obcs_apply_tloc.F & obcs_apply_sloc.F
954    o obcs in model/src:
955      - call OBCS_APPLY_W only if NonHydrostatic.
956      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
957      - reset dEtaHdt and wVel to zero outside OB interior region ;
958      - leave tracer unchanged outside OB interior region: This has no effect
959        on the solution but just to prevent unrealistic tracer value outside OB.
960      - zero out velocity outside OB interior region: This has no effect on
961        the solution but just to prevent unrealistic velocity outside OB.
962    o obcs and non-lin free-surf:
963       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
964       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
965       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
966       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
967       update results of test-exp. exp4(nlfs).
968    o exp4 (nlfs) test-exp:
969       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
970       with NonLin-FreeSurf); update output.nlfs.txt
971    o obcs and 2d/3d solver norm:
972       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
973       and outside OB interior region (will allow to place OB further inside the
974       domain). Depending on the domain, can affects cg2d-Norm (previous
975       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
976       and cg3d-Norm (previous Norm was computed before canceling OB terms),
977       e.g. in tutorial_plume_on_slope.
978      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
979    o pkg rbcs:
980      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
981      - add capability to apply relaxation to horizontal velocity uVel & vVel.
982    o pkg/grdchk: add gradient check for control variable xx_shifwflx
983    o pkg/shelfice/shelfice_init_fixed.F
984      fix CPP-flag combinations
985    o pkg/seaice: Merge iceage code of Pierre Rampal
986      * update/change/correct ice age calculations
987      * add age updates for pathological cases
988      Probably needs more testing...
989    
990    checkpoint62x (2011/05/13)
991    o pkg/mom_vecinv:
992       high-order vorticity scheme: use interior masks (maskInW & S)
993       to zero-out (outside OB) gradient of vorticity.
994    o verification exp.:
995       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
996       hs94.128x64x5 and seaice_obcs ; update results.
997    o pkg/obcs:
998      fix bug in OBeta for YZ sections in obcs_exf_load.F
999    o pkg/ctrl, pkg/shelfice, and optim:
1000      - add new control variable xx_shifwflx (fresh water flux underneath ice
1001        shelves). This is almost as tedious as obcs-ctrl, because the
1002        variables needs its own mask.
1003      - add a cost function term that penalizes the deviation of xx_shifwflx
1004        from the first guess (zero) in analogy to other control variables
1005    o pkg/shelfice:
1006      - start basic adjoint
1007    o pkg/ctrl:
1008      - remove extra 2D field "for good measure" when initializing in
1009        ctrl_set_globfld_[xy/xz/yz].F
1010      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
1011      - improve error messages in ctrl_set_unpack_*
1012    o OBC implementation in momentum:
1013       use interior masks (maskInC,W & S) in momentum S/R:
1014       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
1015       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
1016       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
1017       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
1018       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
1019        (and also with Leith/Smagorinsky harmonic-viscosity).
1020       Update output of experiment dome and exp4 (+nlfs).
1021    o exp4 test-exp:
1022      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
1023        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
1024        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
1025        time-varying OB at Western-side for wVel (NonHyd); update output.
1026      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
1027        and biharmonic-viscosity ; also use prescribed time varying OB.
1028    o pkg/obcs:
1029      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
1030    o model/src:
1031      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
1032      - initialise startTime & nIter0 with unlikely values: allows to set one
1033        from the other without ambiguity.
1034    o seaice_obcs test-exp.:
1035      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
1036    o pkg/obcs:
1037      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
1038        no longer needed with maskInC,W,S in pkg/generic_advdiff.
1039    o pkg/seaice:
1040      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
1041        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
1042      - fixed bug in the initialization of sea ice salinity variable HSALT
1043        in seaice_init_varia.F  (removed dependence on ICE2WATR)
1044    o fizhi-cs test exp.:
1045       switch reference output convention for these 2 non-standard test-exp,
1046        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
1047          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
1048       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
1049    o model/inc:
1050      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
1051        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
1052    o pkg/seaice:
1053      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
1054    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
1055      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
1056        and initial HSALT
1057    
1058    checkpoint62w (2011/04/26)
1059    o pkg/mom_fluxform:
1060      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
1061      - use parameter "sideDragFactor" in no-slip BC side-drag part.
1062      - update output of exp. global_ocean.90x40x15
1063    o pkg/mom_vecinv:
1064      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
1065    o update seaice exp.:
1066      use more consistent parameter values (remove "backward compatability only":
1067       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
1068      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
1069       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
1070    o update test-exp global_ocean.90x40x15:
1071      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
1072      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
1073      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
1074      o turn on zStar & viscA4 in standard set-up (dir input/)
1075        and update output files: output.txt & output.dwnslp.txt
1076    o new AD-test experiment: obcs_ctrl
1077      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
1078    o pkg/dic:
1079      fix two bugs in handling water vapour pressure in carbonate chemistry
1080      and air-sea fluxes. Found by Val Bennington and Galen McKinley
1081      (add DIC Option = WATERVAP_BUG to recover old results)
1082      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
1083    o adding allowInteriorFreezing option to check for water below freezing point
1084      at depth and bring the negative heat anomaly to the surface level
1085    o pkgs _fields_load:
1086      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
1087      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
1088        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
1089        rbcs to get interpolation weights and time reccord number.
1090      - fix multi-threading in aim_fields_load.F
1091      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
1092    o external_fields_load:
1093      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
1094       interpolation weights) to use in a periodic time-series ; do not divide by
1095       time-step to convert to integer:
1096       - this fixes case where externForcingPeriod is not multiple of time-step
1097          (Thanks to Christopher L. Wolfe)
1098       - this fixes case where externForcingPeriod is an odd multiple of time-step
1099         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
1100      store index of time-record which is currently loaded:
1101       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
1102       - needed for the adjoint but not yet used because of extensive recomputations;
1103         (to be fixed soon)
1104    
1105    checkpoint62v (2011/04/02)
1106    o verification/1D_ocean_ice_column added to test Ian Fenty's
1107      pkg/seaice_growth.F modifications for improving sea ice code differentiability
1108    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
1109      (new velocity statistics after changing maskInW & maskInS definition)
1110    o pkg/generic_advdiff with OBCS:
1111      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
1112      equivalent to assumption of no tracer gradient outside the OB region.
1113      This will affect the results if using obcs+biharmonic diffusion.
1114      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
1115    o pkg/obcs:
1116      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
1117      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
1118      in Interior region. No impact on solution but affects Velocity monitor stats.
1119    o pkg/ptracers (adjoint)
1120      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
1121      tape file for each tracer
1122    o model/inc/src and pkg/autodiff: add parameters that allow to turn
1123      of parts of the adjoint code at run time. For now, there are only
1124      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
1125      parameters are set in data.pkg.
1126      This is the lazy coward's version of doing this, but still useful for
1127      debugging. In order to do it right, everything needs to be moved to
1128      pkg/autodiff.
1129    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
1130      the end; this fixes the adjoint balancing code for open boundaries.
1131    o pkg/ctrl:
1132      - change behavior of xx_${varname}period to be analogous to exf-conventions:
1133        xx_${varname}period =   0.,  means time-independent control part
1134        xx_${varname}period = -12., means one-year-periodic monthly control part
1135      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
1136        clean up ctrl_init a little, remove unused variables
1137      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
1138      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
1139    
1140    checkpoint62u (2011/03/15)
1141  o model/src:  o model/src:
1142    - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in    - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
1143      h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;      h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
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